NormToTotalIonAboundances.Rmd

---
title: "NormToTotalIonAboundances"
author: "Mona Khorani"
date: '2023-03-10'
output: html_document
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

```{r}
install.packages("dplyr")

library(tidyverse)
library("dplyr")
library(magrittr)
library(readxl)
library(tidyverse)
library(openxlsx)

```


```{r} 
#get dataset
Raw=read_csv('Raw-145-CM-OutlierRem-HipCortxMix-Pos-NormtoTIA-Progenesis-01March2023-QCCVless30Only - Copy.csv')
```


```{r}
parameters <- data.frame(index = seq_len(76), ColSum = NA, SumDevAvg = NA) # Create an empty data.frame

for (i in 1:76) {
  col_sum <- sum(Raw[1:144, i+1]) # Compute the sum of each column 
  parameters$ColSum[i] <- col_sum # Assign the column sum to the corresponding row of the ColSum column
  parameters$SumDevAvg <- parameters$ColSum/mean(parameters$ColSum) # Divide each sum by the mean of sums and put them on SumDevAvg column on parameters data.frame
}
```


```{r}
empty_df <- data.frame(matrix(nrow = 144, ncol = 76)) # Create an empty data.frame
colnames(empty_df) <- parameters$index

# For loop calculate each value divided by its SumDevAvg and add them to correspondence col and row in empty_df
for (j in 1:76) {
    for (m in 1:144){
     empty_df[m,j] <- Raw[m,j+1]/parameters$SumDevAvg[j]
    }
}

# Save norm to TIA dataset
write.xlsx(empty_df, "NormtoTIA.xlsx")

```



```{r}
# Norm to TIA dataset (to calculate the ratio of the standard deviation to the mean)

parameters1 <- data.frame(index = seq_len(76), ColSum1 = NA, SumDevAvg1 = NA) 
for (i in 1:76) {
  col_sum1 <- sum(empty_df[1:144, i+1]) # Compute the column sum
  parameters1$ColSum1[i] <- col_sum1 # Assign the column sum to the corresponding row of the ColSum column
  parameters1$SumDevAvg1 <- parameters1$ColSum1/mean(parameters1$ColSum1) # Divide each sum by the mean of sums and put them on SumDevAvg column on parameters data.frame
}
```


```{r}
# For Raw dataset
StdDevAvg <- sd(parameters$ColSum)/mean(parameters$ColSum)
StdDevAvg

# For Norm dataset 
StdDevAvg2 <- sd(parameters1$ColSum1)/mean(parameters1$ColSum1)
StdDevAvg2

```